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Name Category Image requires Type interaction level License/Openness has function has topic
APP (All-path pruning) Software APP_Vaa3D_example_results Vaa3D Component Automated Free and open source Filament tracing, Image thresholding, Neuron image analysis Confocal microscopy
APP2 Software APP2_Vaa3D_example_Result Vaa3D Component Automated, Semi-automated Free and open source Filament tracing, Neuron image analysis, Distance transform Confocal microscopy
TReMAP Software Example_TReMAP_Result Vaa3D Component Automated, Semi-automated Free and open source Filament tracing, Image thresholding, Neuron image analysis Confocal microscopy
Rivulet Software Traceplot_Rivulet MATLAB Component Automated, Semi-automated Free and open source Filament tracing, Neuron image analysis Confocal microscopy, Machine learning
wnd-charm Software Generated features Automated Free and open source Image analysis, Shape features, Image feature detection, Analysis Bioimage informatics, Machine learning
CIDRE Software Illumination correction method ImageJ, MATLAB Collection Automated Free and open source Illumination correction High content screening, Light microscopy
hIPNAT Software need a thumbnail ImageJ Collection Semi-automated Free and open source Filament tracing, Neuron image analysis, Object feature extraction Bioimage informatics
KNIME Image Processing and Analysis Software Knime ImageJ, ICY Annotation, Graph Cut, OMERO, Bio-Formats, KNIME Anisotropic Diffusion , Processing, Image Calculator (KNIME), Image Normalizer (KNIME), ImgLib2, ImgLib2, Max Filter (KNIME), Max Homogeneity (KNIME), Quantile Filter (KNIME), Sigma Filter, Sigma Filter, Sobel Filter (KNIME), KNIME Variance Filter Collection Automated Free and open source
WIS-NeuroMath Software MATLAB Collection Automated Free and open source Image segmentation
VIGRA Software Collection Automated Free and open source Texture extraction, Classification, Geometrical transformation, Image convolution, Morphological operation Bioimage informatics, Machine learning
WIS-PhagoTracker Software MATLAB Collection Automated Free but not open source Image segmentation, Object tracking Bioimage informatics
CellCognition Software Cell Cognition logo Segmentation of Clustered Cells in MATLAB, ICY Annotation Collection Automated Free and open source
PALMsiever Software PalmSiever logo MATLAB Collection Automated, Manual Free and open source Analysis, Visualisation Super-resolution microscopy
OMERO Software Omero OMERO Collection Manual Free and open source Data handling, Image annotation Bioimage informatics, Data sharing
Fiji Software Fiji Collection Automated Free and open source
ImgLib2 Software need a thumbnail ImageJ Collection Manual Free and open source Bioimage informatics
Icy Software Icy Collection Automated, Manual, Semi-automated Free and open source
Definiens Developer Software need a thumbnail Collection Automated Commercial
FARSIGHT Software need a thumbnail Segmentation of Clustered Cells in MATLAB Collection Automated Free and open source
Mahotas Software Python, NumPy Collection Free and open source Image classification, Image thresholding, Watershed segmentation, Shape features, Morphological operation, Image processing